2Current leukemia therapies target cancer cells with specific phenotypes or genotypes, but this 3 assumes that either genomic mutations or immunophenotypes alone serve as faithful proxies for 4 treatment response 1 . Moreover, the heterogeneity inherent to all cancers, including leukemias, 5 makes direct mapping of genotype-phenotype relationships challenging 2,3 . Here, we present a 6 method to genotype and phenotype single cells at high throughput, allowing direct characterization 7 of proteogenomic states on tens of thousands of cancer cells rapidly and cost efficiently. Using the 8 approach, we analyze the disease of three leukemia patients over multiple treatment timepoints 9 and recurrences. We observe complex genotype-phenotype dynamics and extensive decoupling of 10 the relationships over disease progression and response to therapy, illustrating the subtlety of the 11 disease process and the inability to use genotypes as direct proxies for phenotypes. Our technology 12 has enabled the first rigorous test of the prevailing paradigm that treatment of a disease phenotype 13 is equivalent to treatment of its underlying genotype. More broadly, our results highlight the power 14 of single-cell multiomic measurements to resolve complex biology in heterogeneous populations, 15 and illustrate how this information can be used to inform treatment. We thus expect that our 16 methodology will find broad application to study proteogenomic tumor landscapes across cancers 17 and will support the next generation of immunotherapy. 18 19 20 Main 21 22 42 aberrations such as single nucleotide polymorphisms (SNPs) and gene fusions 13 . Single-cell RNA 43 sequencing (scRNA-seq) has emerged as a potentially valuable approach for genotype-phenotype 44 linkage because it is cost effective and scalable 3,10,14,15 . The mRNA sequences provide genotype 45 information 15,16 while their counts relate phenotype 17-21 . Moreover, modern approaches are 46 extremely high throughput, allowing characterization of thousands of cells. Nevertheless, 47